This invention is in the general area of genetic engineering of nucleic acid sequences, especially RNA sequences that are substrates for ribozyme activity derived from Ribonuclease P.
Discoveries in the realm of molecular biology over the past five years have led to the realization that RNA has a series of distinct capabilities and biological activities previously unsuspected. The most important of these novel RNA-level discoveries has been the finding that RNA can be an enzyme as well as an information carrier.
There are five classes of ribozymes now known which are involved in the cleavage and/or ligation of RNA chains. A ribozyme is defined as an enzyme which is made of RNA, most of which work on RNA substrates. Ribozymes have been known since 1982, when Cech and colleagues (Cell, 31:147-157) showed that a ribosomal RNA precursor in Tetrahymena, a unicellular eukaryote, undergoes cleavage catalyzed by elements in the RNA sequence to be removed during the conversion of the rRNA precursor into mature rRNA. This sequence to be removed (called an intervening sequence or intron) is one of what are now known to be numerous examples of "Class I" intron ribozyme activities. A similar "Class II" intron ribozyme mechanism was discovered more recently, involving the cleavage and subsequent ligation of a number of yeast mitochondrial RNAs (Nature, 324:429-433 1987). Cech and colleagues described certain in vitro applications of "class I" ribozymes in PCT/US887/03161 by University Patents, Inc., (published as WO 88/04300 Jun. 16, 1988). Their potential for therapeutic applications in cells and in patients remains unclear.
A third class of ribozyme, discovered in 1983, was the first to be shown to work in trans (i.e., to work under conditions where the ribozyme is built into one RNA chain while the substrate to be cleaved is a second, separate RNA chain). This ribozyme, called M1 RNA, was characterized in 1983 by Altman and colleagues as responsible for the cleavage which forms mature 5' ends of all transfer RNAs (tRNAs) in E. coli. Analogous RNA-containing enzymes concerned with tRNA synthesis have since been found in all cells in which they have been sought, including a number of human cell lines, though the relevant eucaryotic RNAs have not yet been shown to be catalytic by themselves in vitro.
The discovery and characterization of this catalytic RNA is reviewed by Sidney Altman, in "Ribonuclease P: An Enzyme with a Catalytic RNA Subunit" in Adv. Enzymol. 62, 1-36 (1989). The activity was first isolated from E. coli extracts, and subsequently determined to be a ribonucleoprotein having two components, an RNA component called M1 and a protein component called C5. The RNA cleaved substrates in a true enzymatic reaction, as measured using Michaelis-Menton kinetics. M1 was determined to be solely responsible for substrate recognition and C5 was determined to alter k.sub.cat but not K.sub.M, as reported by Guerrier-Takada, et al., Cell 35, 849 (1983) and McClain, et al., Science 238, 527 (1987). Sequencing showed that M1 RNA is 377 nucleotides long, M.sub.r approximately 125,000, and that the protein consists of 119 amino acids, M.sub.r approximately 13,800, as reported by Hansen, et al., Gene 38, 535 (1987).
The two remaining ribozyme classes are related to the replication cycle of a group of self-replicating RNAs called "viroid-like pathogens", or VLPs. Plant viroids, RNA satellites of plant viruses, and Hepatitis delta virus are all members of the VLP group. The VLPs can be divided into two classes: Class I, free living viroids; and Class II, including virusoids and satellite viroids (RNA molecules which require a helper virus to replicate). The hepatitis delta virus is a Class II VLP by this definition.
In 1984, Branch and Robertson (Science, 233:450-455) published the replication cycle strategies for these pathogens, subsequently verified by experiments conducted in several laboratories. A key element of this "rolling-circle" replication strategy is that the VLP undergoing replication makes greater-than-unit-length copies of its information, which are then cleaved to monomeric size by ribozyme activities built into the RNA of the VLP itself. Sharmeen at. al., J. Virol., 62, 2674-2679 (1988); Branch, et. al., Science. 243, 649-652 (1989); and Wu and Lai, Science 243, 652-655 (1989), defined the ribozyme cleavage points of both delta strands and the domains containing them for hepatitis delta virus.
One type of VLP ribozymes is defined by a small structural domain, consisting of only about 30 nucleotides, called a "hammerhead". Uhlenbeck, Nature (1987), first developed these small (as few as 18 nucleotides) and relatively specific ribozyme sequences from plant viroids such as avocado sunblotch viroid and the satellite RNAs of tobacco ringspot virus and lucerne transient streak virus. Uhlenbeck (1987) and Forster and Symons (Cell 50, 9-16, 1987), defined the requirements for cleavage by this ribozyme class. Various embodiments and potential applications have also been described by Haseloff, Gerlach and Jennings in PCT/AU88/00478 by Commonwealth Scientific and Industrial Research Organization (published as WO 90/05852 29 Jun. 1989).
All reactions that are governed by RNA in vivo result in the transesterification or hydrolysis of specific phosphodiester bonds in RNA. In several classes of these reactions, an intramolecular site of cleavage or ligation is identified by internal guide sequences (IGSs) which form base pairs with the segment of the phosphodiester chain that contains the cleavage site. The Tetrahymena sequence, as well as the subsequently discovered sequence in yeast, is not a true enzyme since it is not regenerated in the process but instead acts in a stoichiometric ratio. Although it is possible to engineer fragments of this sequence which have enzymatic activity under certain conditions in vitro and are able to cleave and ligate RNA, a disadvantage to these fragments is that they are very large (requiring more than 200 residues of the original 415 nucleotide sequence) and of limited specificity. In their present forms, the Tetrahymena ribozymes have four-base recognition sequences and the hammerhead ribozymes have approximately 12-base recognition sequences. The likelihood of an RNA the size of a typical mRNA containing a particular four-base sequence is much greater than the likelihood of the RNA containing a 12-base sequences, allowing these ribozymes to be used in a complementary fashion to cleave RNA.
IGSs are not present in one class of reactions governed by RNA that is enzymatic in vivo, cleavage of precursor tRNA molecules by the RNA component of eubacterial RNase P, described by Guerrier-Takada, et al., Cell 35, 849 (1983) and reviewed by Altman, Adv. Enzymol. 62, 1 (1989). The nucleotide sequence of the segment of the phosphodiester chain that contains the cleavage site is not conserved among different substrates for RNase P, so it cannot be recognized as a unique IGS for the enzyme.
There have been a number of suggestions in the literature that ribozymes may have utility as reagents or as therapeutic agents, although little has been accomplished in implementing this goal. The key knowledge for harnessing any class of ribozyme, i.e., knowledge of its detailed, primary, secondary, and tertiary structure resulting in understanding its mechanism, and similar data regarding its substrate and the substrate recognition process, has yet to be acquired.
It is therefore an object of the present invention to provide methods and compositions for specifically cleaving targeted RNA sequences using RNase P or functional equivalents thereof.
It is a further object of the present invention to provide methods and compositions for specifically cleaving RNA, both in vitro and in vivo, for the treatment of disease conditions which involve RNA transcription or translation, such as diseases caused by RNA and DNA viruses and expression of excessive or pathogenic proteins from mRNA.